Functional Analysis

Gaf Domain

New avenues in protein function prediction http://www.proteinscience.org/cgi/content/full/15/6/1527

Sequence -> Function

• Detecting Protein Function and Protein-Protein Interactions from Genome Sequences

Edward M. Marcotte, Matteo Pellegrini, Ho-Leung Ng, Danny W. Rice, Todd O. Yeates, and David Eisenberg (30 July 1999) Science 285 (5428), 751. [DOI: 10.1126/science.285.5428.751] [1]

Structure -> Function

• Proknow

Pal D and Eisenberg D. (2005). Inference of protein function from protein structure. Structure 13, 121-130. [2]

• Profunc [3]

Laskowski R A, Watson J D, Thornton J M (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93. [4]

Results:

Locate http://locate.imb.uq.edu.au LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM3 mouse protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.

2gnx BlastP

STRING: a database of predicted functional associations between proteins. String returned no results.

CDART http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps - when given a protein query sequence, CDART displays the functional domains that make up the protein and lists proteins with similar domain architectures. Returns no results for mouse sequence.

Pfam didn't work...http://www.sanger.ac.uk/cgi-bin/Pfam/getblast?id=2103981H86007039eB664 - protein families

Profunc http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=ay41&code=073806

Interpro returned no results - protein domain prediction.

Mammalian Orthology http://www.informatics.jax.org/searches/homology_report.cgi?_Marker_key=92352 -- Genes

Mammalian Orthology http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids=17580 --Proteins

GEGG biochemical pathways

KEGG pathways which involve cAMP

MicroArray Analysis

Entrez gene ID 270802 1. click link to 270802 2. click link to symatlas 3. find correlated

Symatlas is a database full of microarray data for genes in different tissues. It has the function to find correlated microarray data which brings up genes with similar expression data.

The results of a correlation search give a fair few corresponding genes with similar microarray expressions, however the presence of several olfactory receptors seemed interesting : Olfr435, Olfr57, Olfr829, Olfr30.

As the structural team have found a GAF domain on the C-terminal, i tried to find a link between olfactory receptors and the GAF domain. - related to cGMP and PDEs???

Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor

cis-regulatory elements

Cis Red - The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. regulatory elements in BC048403

Annotation-based Co-occurring Motif Pattern

[5]

aire-foxj2

pax6-pax6

pou1f1-pax6

ipf1-pou1f1

The following table portrays the entire 120 olfactory receptors corresponding to the 14 modules listed accross the top. This table has been cut down to olfactory receptors that have 3 or more co-occuring modules, and is presented in the report.

cdx-2_IPF1

AFP1_POU2F1

AIRE_FOXJ2

cdx-2_foxj2

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

aire_ipf1

ipf1_pax-6

afp1_pou1f1

afp1_pax-6

afpa_ipf1

pax-6_pax-6

ipf1_pou1f1

count

olfactory receptor 39 [Source:MarkerSymbol;Acc:MGI:1313142]

ipf1_pou2f1

1

olfactory receptor 43 [Source:MarkerSymbol;Acc:MGI:1333770]

AFP1_POU2F1

pou2f1_pax-6

2

olfactory receptor 58 [Source:MarkerSymbol;Acc:MGI:1333790]

AFP1_POU2F1

pou2f1_pax-6

afp1_pax-6

3

olfactory receptor 104 [Source:MarkerSymbol;Acc:MGI:2177487]

pou2f1_pax-6

1

olfactory receptor 116 [Source:MarkerSymbol;Acc:MGI:2177499]

AIRE_FOXJ2

1

olfactory receptor 123 [Source:MarkerSymbol;Acc:MGI:2177506]

ipf1_pou2f1

1

olfactory receptor 127 [Source:MarkerSymbol;Acc:MGI:2177510]

pou2f1_pax-6

1

olfactory receptor 135 [Source:MarkerSymbol;Acc:MGI:2177518]

afp1_pou1f1

1

olfactory receptor 146 [Source:MarkerSymbol;Acc:MGI:2660711]

ipf1_pou2f1

1

olfactory receptor 153 [Source:MarkerSymbol;Acc:MGI:1313138]

cdx-2_IPF1

AFP1_POU2F1

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

afp1_pou1f1

afp1_pax-6

afpa_ipf1

ipf1_pou1f1

9

olfactory receptor 168 [Source:MarkerSymbol;Acc:MGI:3030002]

cdx-2_IPF1

1

olfactory receptor 169 [Source:MarkerSymbol;Acc:MGI:3030003]

cdx-2_IPF1

AFP1_POU2F1

ipf1_pou2f1

pou2f1_pax-6

afp1_pax-6

ipf1_pou1f1

6

olfactory receptor 170 [Source:MarkerSymbol;Acc:MGI:3030004]

ipf1_pou2f1

pou2f1_pax-6

2

olfactory receptor 171 [Source:MarkerSymbol;Acc:MGI:3030005]

pou1f1_pax-6

aire_ipf1

ipf1_pax-6

pax-6_pax-6

ipf1_pou1f1

5

olfactory receptor 172 [Source:MarkerSymbol;Acc:MGI:3030006]

cdx-2_foxj2

olfactory receptor 178 [Source:MarkerSymbol;Acc:MGI:3030012]

ipf1_pou2f1

aire_ipf1

2

olfactory receptor 180 [Source:MarkerSymbol;Acc:MGI:3030014]

AIRE_FOXJ2

afp1_pou1f1

2

olfactory receptor 181 [Source:MarkerSymbol;Acc:MGI:3030015]

ipf1_pou2f1

pou2f1_pax-6

2

olfactory receptor 183 [Source:MarkerSymbol;Acc:MGI:3030017]

ipf1_pou2f1

1

olfactory receptor 192 [Source:MarkerSymbol;Acc:MGI:3030026]

ipf1_pou2f1

aire_ipf1

2

olfactory receptor 193 [Source:MarkerSymbol;Acc:MGI:3030027]

afp1_pou1f1

1

olfactory receptor 196 [Source:MarkerSymbol;Acc:MGI:3030030]

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

ipf1_pax-6

ipf1_pou1f1

5

olfactory receptor 204 [Source:MarkerSymbol;Acc:MGI:3030038]

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

ipf1_pax-6

4

olfactory receptor 205 [Source:MarkerSymbol;Acc:MGI:3030039]

cdx-2_foxj2

ipf1_pou2f1

1

olfactory receptor 295 [Source:MarkerSymbol;Acc:MGI:3030129]

ipf1_pou2f1

pou2f1_pax-6

ipf1_pax-6

3

olfactory receptor 303 [Source:MarkerSymbol;Acc:MGI:3030137]

pou2f1_pax-6

1

olfactory receptor 310 [Source:MarkerSymbol;Acc:MGI:3030144]

cdx-2_IPF1

ipf1_pou2f1

ipf1_pou1f1

3

olfactory receptor 320 [Source:MarkerSymbol;Acc:MGI:3030154]

afpa_ipf1

1

olfactory receptor 339 [Source:MarkerSymbol;Acc:MGI:3030173]

cdx-2_IPF1

ipf1_pou2f1

2

olfactory receptor 342 [Source:MarkerSymbol;Acc:MGI:3030176]

aire_ipf1

1

olfactory receptor 385 [Source:MarkerSymbol;Acc:MGI:3030219]

0

AFP1_POU2F1

afp1_pou1f1

2

olfactory receptor 447 [Source:MarkerSymbol;Acc:MGI:3030281]

pou2f1_pax-6

1

olfactory receptor 469 [Source:MarkerSymbol;Acc:MGI:3030303]

ipf1_pou1f1

1

olfactory receptor 487 [Source:MarkerSymbol;Acc:MGI:3030321]

pou1f1_pax-6

1

olfactory receptor 488 [Source:MarkerSymbol;Acc:MGI:3030322]

AFP1_POU2F1

1

olfactory receptor 493 [Source:MarkerSymbol;Acc:MGI:3030327]

AFP1_POU2F1

cdx-2_foxj2

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

afp1_pou1f1

afp1_pax-6

afpa_ipf1

pax-6_pax-6

9

olfactory receptor 494 [Source:MarkerSymbol;Acc:MGI:3030328]

ipf1_pou1f1

1

olfactory receptor 495 [Source:MarkerSymbol;Acc:MGI:3030329]

cdx-2_IPF1

aire_ipf1

ipf1_pou1f1

3

olfactory receptor 498 [Source:MarkerSymbol;Acc:MGI:3030332]

cdx-2_IPF1

ipf1_pou1f1

2

olfactory receptor 502 [Source:MarkerSymbol;Acc:MGI:3030336]

cdx-2_IPF1

ipf1_pou2f1

pou2f1_pax-6

aire_ipf1

ipf1_pax-6

pax-6_pax-6

6

olfactory receptor 508 [Source:MarkerSymbol;Acc:MGI:3030342]

ipf1_pou2f1

1

olfactory receptor 509 [Source:MarkerSymbol;Acc:MGI:3030343]

cdx-2_foxj2

1

olfactory receptor 510 [Source:MarkerSymbol;Acc:MGI:3030344]

cdx-2_IPF1

cdx-2_foxj2

ipf1_pou2f1

ipf1_pou1f1

3

olfactory receptor 512 [Source:MarkerSymbol;Acc:MGI:3030346]

ipf1_pou2f1

aire_ipf1

2

olfactory receptor 516 [Source:MarkerSymbol;Acc:MGI:3030350]

pou1f1_pax-6

1

olfactory receptor 645 [Source:MarkerSymbol;Acc:MGI:3030479]

afp1_pou1f1

1

olfactory receptor 666 [Source:MarkerSymbol;Acc:MGI:3030500]

afp1_pou1f1

1

olfactory receptor 715 [Source:MarkerSymbol;Acc:MGI:3030549]

AFP1_POU2F1

1

olfactory receptor 723 [Source:MarkerSymbol;Acc:MGI:3030557]

afp1_pou1f1

afpa_ipf1

ipf1_pou1f1

3

olfactory receptor 724 [Source:MarkerSymbol;Acc:MGI:3030558]

ipf1_pou2f1

ipf1_pou1f1

2

olfactory receptor 765 [Source:MarkerSymbol;Acc:MGI:3030599]

pou2f1_pax-6

1

olfactory receptor 771 [Source:MarkerSymbol;Acc:MGI:3030605]

AIRE_FOXJ2

cdx-2_foxj2

1

olfactory receptor 772 [Source:MarkerSymbol;Acc:MGI:3030606]

AIRE_FOXJ2

1

olfactory receptor 774 [Source:MarkerSymbol;Acc:MGI:3030608]

cdx-2_foxj2

1

olfactory receptor 777 [Source:MarkerSymbol;Acc:MGI:3030611]

cdx-2_IPF1

ipf1_pou1f1

2

olfactory receptor 798 [Source:MarkerSymbol;Acc:MGI:3030632]

cdx-2_IPF1

1

olfactory receptor 800 [Source:MarkerSymbol;Acc:MGI:3030634]

cdx-2_IPF1

cdx-2_foxj2

ipf1_pou2f1

2

olfactory receptor 801 [Source:MarkerSymbol;Acc:MGI:3030635]

ipf1_pou2f1

1

olfactory receptor 803 [Source:MarkerSymbol;Acc:MGI:3030637]

AFP1_POU2F1

AIRE_FOXJ2

ipf1_pou2f1

aire_ipf1

4

olfactory receptor 804 [Source:MarkerSymbol;Acc:MGI:3030638]

AIRE_FOXJ2

ipf1_pou2f1

aire_ipf1

ipf1_pou1f1

4

olfactory receptor 806 [Source:MarkerSymbol;Acc:MGI:3030640]

AIRE_FOXJ2

aire_ipf1

afpa_ipf1

3

olfactory receptor 814 [Source:MarkerSymbol;Acc:MGI:3030648]

cdx-2_IPF1

AFP1_POU2F1

cdx-2_foxj2

ipf1_pou2f1

pou2f1_pax-6

ipf1_pax-6

afp1_pax-6

afpa_ipf1

7

olfactory receptor 815 [Source:MarkerSymbol;Acc:MGI:3030649]

pou2f1_pax-6

ipf1_pax-6

2

olfactory receptor 816 [Source:MarkerSymbol;Acc:MGI:3030650]

ipf1_pou1f1

1

olfactory receptor 821 [Source:MarkerSymbol;Acc:MGI:3030655]

ipf1_pou2f1

ipf1_pou1f1

2

olfactory receptor 826 [Source:MarkerSymbol;Acc:MGI:3030660]

ipf1_pou2f1

pou1f1_pax-6

ipf1_pax-6

afp1_pou1f1

afp1_pax-6

afpa_ipf1

ipf1_pou1f1

7

olfactory receptor 862 [Source:MarkerSymbol;Acc:MGI:3030696]

ipf1_pou1f1

1

olfactory receptor 945 [Source:MarkerSymbol;Acc:MGI:3030779]

AIRE_FOXJ2

1

olfactory receptor 951 [Source:MarkerSymbol;Acc:MGI:3030785]

ipf1_pou1f1

1

olfactory receptor 965 [Source:MarkerSymbol;Acc:MGI:3030799]

AIRE_FOXJ2

1

olfactory receptor 971 [Source:MarkerSymbol;Acc:MGI:3030805]

aire_ipf1

afpa_ipf1

2

olfactory receptor 1014 [Source:MarkerSymbol;Acc:MGI:3030848]

AFP1_POU2F1

afp1_pou1f1

ipf1_pou1f1

3

olfactory receptor 1029 [Source:MarkerSymbol;Acc:MGI:3030863]

pou1f1_pax-6

afp1_pax-6

pax-6_pax-6

0

3

olfactory receptor 1030 [Source:MarkerSymbol;Acc:MGI:3030864]

ipf1_pou2f1

aire_ipf1

ipf1_pax-6

3

olfactory receptor 1032 [Source:MarkerSymbol;Acc:MGI:3030866]

AFP1_POU2F1

1

olfactory receptor 1036 [Source:MarkerSymbol;Acc:MGI:3030870]

AFP1_POU2F1

1

olfactory receptor 1071 [Source:MarkerSymbol;Acc:MGI:3030905]

pou1f1_pax-6

pou2f1_pax-6

2

olfactory receptor 1094 [Source:MarkerSymbol;Acc:MGI:3030928]

AIRE_FOXJ2

ipf1_pou2f1

2

olfactory receptor 1115 [Source:MarkerSymbol;Acc:MGI:3030949]

AFP1_POU2F1

1

olfactory receptor 1116 [Source:MarkerSymbol;Acc:MGI:3030950]

cdx-2_IPF1

AFP1_POU2F1

ipf1_pou2f1

3

olfactory receptor 1121 [Source:MarkerSymbol;Acc:MGI:3030955]

cdx-2_IPF1

ipf1_pou2f1

2

olfactory receptor 1123 [Source:MarkerSymbol;Acc:MGI:3030957]

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

ipf1_pax-6

ipf1_pou1f1

5

olfactory receptor 1126 [Source:MarkerSymbol;Acc:MGI:3030960]

cdx-2_foxj2

olfactory receptor 1129 [Source:MarkerSymbol;Acc:MGI:3030963]

cdx-2_IPF1

ipf1_pou1f1

2

olfactory receptor 1130 [Source:MarkerSymbol;Acc:MGI:3030964]

cdx-2_IPF1

ipf1_pou1f1

2

olfactory receptor 1131 [Source:MarkerSymbol;Acc:MGI:3030965]

pou1f1_pax-6

pou2f1_pax-6

2

olfactory receptor 1140 [Source:MarkerSymbol;Acc:MGI:3030974]

ipf1_pou2f1

ipf1_pou1f1

2

olfactory receptor 1145 [Source:MarkerSymbol;Acc:MGI:3030979]

AFP1_POU2F1

ipf1_pou2f1

2

olfactory receptor 1148 [Source:MarkerSymbol;Acc:MGI:3030982]

pou1f1_pax-6

afp1_pou1f1

2

olfactory receptor 1151 [Source:MarkerSymbol;Acc:MGI:3030985]

AFP1_POU2F1

ipf1_pou2f1

afp1_pou1f1

ipf1_pou1f1

4

olfactory receptor 1152 [Source:MarkerSymbol;Acc:MGI:3030986]

ipf1_pou2f1

pou1f1_pax-6

ipf1_pax-6

ipf1_pou1f1

4

olfactory receptor 1153 [Source:MarkerSymbol;Acc:MGI:3030987]

cdx-2_IPF1

ipf1_pou2f1

afpa_ipf1

ipf1_pou1f1

4

olfactory receptor 1161 [Source:MarkerSymbol;Acc:MGI:3030995]

cdx-2_IPF1

pou1f1_pax-6

aire_ipf1

ipf1_pax-6

afp1_pou1f1

afpa_ipf1

ipf1_pou1f1

7

olfactory receptor 1178 [Source:MarkerSymbol;Acc:MGI:3031012]

AFP1_POU2F1

afp1_pou1f1

2

olfactory receptor 1184 [Source:MarkerSymbol;Acc:MGI:3031018]

cdx-2_IPF1

1

olfactory receptor 1189 [Source:MarkerSymbol;Acc:MGI:3031023]

ipf1_pax-6

1

olfactory receptor 1193 [Source:MarkerSymbol;Acc:MGI:3031027]

cdx-2_IPF1

AIRE_FOXJ2

2

olfactory receptor 1202 [Source:MarkerSymbol;Acc:MGI:3031036]

afpa_ipf1

0

ipf1_pou1f1

2

olfactory receptor 1203 [Source:MarkerSymbol;Acc:MGI:3031037]

0

AFP1_POU2F1

1

olfactory receptor 1257 [Source:MarkerSymbol;Acc:MGI:3031091]

ipf1_pou2f1

pou2f1_pax-6

ipf1_pax-6

ipf1_pou1f1

4

olfactory receptor 1259 [Source:MarkerSymbol;Acc:MGI:3031093]

ipf1_pou1f1

1

olfactory receptor 1276 [Source:MarkerSymbol;Acc:MGI:3031110]

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

ipf1_pax-6

ipf1_pou1f1

5

olfactory receptor 1278 [Source:MarkerSymbol;Acc:MGI:3031112]

cdx-2_foxj2

ipf1_pou1f1

1

olfactory receptor 1279 [Source:MarkerSymbol;Acc:MGI:3031113]

ipf1_pou1f1

1

olfactory receptor 1283 [Source:MarkerSymbol;Acc:MGI:3031117]

ipf1_pou1f1

1

olfactory receptor 1287 [Source:MarkerSymbol;Acc:MGI:3031121]

ipf1_pou1f1

1

olfactory receptor 1302 [Source:MarkerSymbol;Acc:MGI:3031136]

cdx-2_foxj2

olfactory receptor 1362 [Source:MarkerSymbol;Acc:MGI:3031196]

afp1_pou1f1

1

olfactory receptor 1406 [Source:MarkerSymbol;Acc:MGI:3031240]

pou2f1_pax-6

1

olfactory receptor 1426 [Source:MarkerSymbol;Acc:MGI:3031260]

ipf1_pou1f1

1

olfactory receptor 1436 [Source:MarkerSymbol;Acc:MGI:3031270]

cdx-2_IPF1

1

olfactory receptor 1448 [Source:MarkerSymbol;Acc:MGI:3031282]

cdx-2_foxj2

pou2f1_pax-6

pax-6_pax-6

2

olfactory receptor 1451 [Source:MarkerSymbol;Acc:MGI:3031285]

afp1_pou1f1

1

olfactory receptor 1457 [Source:MarkerSymbol;Acc:MGI:3031291]

ipf1_pou2f1

pou1f1_pax-6

pou2f1_pax-6

ipf1_pax-6

ipf1_pou1f1

5

olfactory receptor 1480 [Source:MarkerSymbol;Acc:MGI:3031314]

ipf1_pou2f1

1

olfactory receptor 1495 [Source:MarkerSymbol;Acc:MGI:3031329]

afp1_pax-6

1

olfactory receptor 1508 [Source:MarkerSymbol;Acc:MGI:3031342]

AIRE_FOXJ2

1

olfactory receptor 1510 [Source:MarkerSymbol;Acc:MGI:3031344]

pou2f1_pax-6

1

Olfactory receptor MOR218-3. [Source:Uniprot/SPTREMBL;Acc:Q8VF67]

AFP1_POU2F1

1

22

20

12

119

43

17

27

13

16

17

8

11

5

38

250

Return to Hypothetical protein LOC144577